Hostname: page-component-cd9895bd7-8ctnn Total loading time: 0 Render date: 2024-12-26T04:58:29.341Z Has data issue: false hasContentIssue false

Sequence Matters: Genomic Research and the Gene Concept

Published online by Cambridge University Press:  01 January 2022

Abstract

Analysis of two key ways of characterizing genes—as causes of phenotypic effects and as genomic DNA sequences—has yielded widespread pessimism that they can be united in a coherent gene concept. This raises important questions about the epistemology of genomic research: If analysis of a genome sequence cannot yield information about genes defined both in terms of their products and their DNA sequence, then what could we learn from it? I investigate basic tools of genomic analysis, argue that they do not reflect the application of either gene concept, and clarify how we learn from genomic research.

Type
Research Article
Copyright
Copyright © The Philosophy of Science Association

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

I wish to thank Cheryl Kerfeld, André Cavalcanti, and James Lennox for their help with this project.

References

Barnes, Barry, and Dupré, John. 2008. Genomes and What to Make of Them. Chicago: University of Chicago Press.CrossRefGoogle Scholar
Burian, Richard M. 2005. “Too Many Kinds of Genes? Some Problems Posed by Discontinuities in Gene Concepts and the Continuity of the Genetic Material (1995).” In The Epistemology of Development, Evolution, and Genetics: Selected Essays, ed. Burian, Richard, 166–78. New York: Cambridge University Press.Google Scholar
Downes, Stephen. 2004. “Alternative Splicing, the Gene Concept, and Evolution.” History and Philosophy of the Life Sciences 26:91104.CrossRefGoogle ScholarPubMed
Eddy, Sean R. 2004. “What Is a Hidden Markov Model?Nature Biotechnology 22:1315–16.CrossRefGoogle ScholarPubMed
Filichkin, Sergei A., Priest, H. D., Givan, S. A., Shen, R., Bryant, D. W., Fox, S., Wong, W. K., and Mochler, T. C.. 2010. “Genome-Wide Mapping of Alternative Splicing in Arabidopsis Thaliana.Genome Research 20:4558.CrossRefGoogle ScholarPubMed
Fogle, Thomas. 2000. “The Dissolution of Protein Coding Genes in Molecular Biology.” In The Concept of the Gene in Development and Evolution: Historical and Epistemological Perspectives, ed. Beurton, Peter, Falk, Raphael, and Rheinberger, Hans-Jörg, 325. New York: Cambridge University Press.CrossRefGoogle Scholar
Griffiths, Paul E., and Stotz, Karola. 2007. “Gene.” In Cambridge Companion to the Philosophy of Biology, ed. Hull, David L. and Ruse, Micael, 85102. New York: Cambridge University Press.CrossRefGoogle Scholar
Higgs, Paul G., and Attwood, Teresa K.. 2005. Bioinformatics and Molecular Evolution. Malden, MA: Blackwell.Google Scholar
Joint Genome Institute. 2011. Genome projects, U.S. Department of Energy, Washington, DC, http://www.jgi.doe.gov/genome-projects.Google Scholar
Lunter, Gerton, Rocco, A., Mimouni, N., Heger, A., Caldeira, A., and Hein, J.. 2008. “Uncertainty in Homology Inferences: Assessing and Improving Genomic Sequence Alignment.” Genome Research 18:298309.CrossRefGoogle ScholarPubMed
Moss, Lenny. 2003. What Genes Can’t Do. Cambridge, MA: MIT Press.Google Scholar
Moss, Lenny. 2006. “Redundancy, Plasticity, and Detachment: The Implications of Comparative Genomics for Evolutionary Thinking.” Philosophy of Science 73:930–46.CrossRefGoogle Scholar
Mount, David W. 2001. Bioinformatics: Sequence and Genome Analysis. New York: Cold Spring Harbor Laboratory.Google Scholar
National Center for Biotechnology Information. 2011. BLAST (Basic Local Alignment Search Tool), U.S. National Library of Medicine, Bethesda, MD, http://blast.ncbi.nlm.nih.gov/Blast.cgi.Google Scholar
Piotrowska, Monika. 2009. “What Does It Mean to Be 75% Pumpkin? The Units of Comparative Genomics.” Philosophy of Science 76:838–50.CrossRefGoogle Scholar
Stotz, Karola, Bostanci, Adam, and Griffiths, Paul E.. 2006. “Tracking the Shift to ‘Post-genomics.” Community Genetics 9:190–96.Google Scholar